int TrajinList::AddTrajin(std::string const& fname, Topology* topIn, ArgList const& argIn)
{
if (topIn == 0) {
mprinterr("Error: No topology for input trajectory '%s'\n", fname.c_str());
return 1;
}
// CRDIDXARG
finalCrdIndicesArg_.clear();
ArgList trajin_args = argIn;
bool isRemdtraj = trajin_args.hasKey("remdtraj");
int err = 0;
File::NameArray fnames = File::ExpandToFilenames( fname );
if (fnames.empty()) return 1;
Trajin* traj = 0;
for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
ArgList args = trajin_args;
if (isRemdtraj)
traj = new Trajin_Multi();
else
traj = new Trajin_Single();
if (traj == 0) {
mprinterr("Error: Memory allocation for input trajectory failed.\n");
return 1;
}
traj->SetDebug(debug_);
if ( traj->SetupTrajRead(*fn, args, topIn) ) {
mprinterr("Error: Could not set up input trajectory '%s'.\n", fn->full());
delete traj;
err++;
continue;
}
// Add to trajin list and update # of frames.
trajin_.push_back( traj );
UpdateMaxFrames( traj->Traj() );
}
if (err > 0) return 1;
// FIXME: For backwards compat. overwrite Topology box info with traj box info.
topIn->SetBoxFromTraj( trajin_.back()->TrajCoordInfo().TrajBox() );
return 0;
}
Exec::RetType Exec_ReadData::Execute(CpptrajState& State, ArgList& argIn) {
DataFile dataIn;
dataIn.SetDebug( State.DFL().Debug() );
std::string filenameIn = argIn.GetStringNext();
File::NameArray fnames = File::ExpandToFilenames( filenameIn );
if (fnames.empty()) {
mprinterr("Error: '%s' matches no files.\n", filenameIn.c_str());
return CpptrajState::ERR;
}
int err = 0;
int idx = -1;
bool useIndex = argIn.hasKey("separate");
for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
if (useIndex) idx++;
if (dataIn.ReadDataIn( *fn, argIn, State.DSL(), idx, fnames.size() )!=0) {
mprinterr("Error: Could not read data file '%s'.\n", fn->full());
err++;
}
}
if (err > 0) return CpptrajState::ERR;
return CpptrajState::OK;
}
// TrajinList::AddEnsembleIn()
int TrajinList::AddEnsembleIn(std::string const& fname, Topology* topIn, ArgList const& argIn)
{
if (topIn == 0) {
mprinterr("Error: No topology for input ensemble '%s'\n", fname.c_str());
return 1;
}
int err = 0;
File::NameArray fnames = File::ExpandToFilenames( fname );
if (fnames.empty()) return 1;
TrajectoryFile::TrajFormatType trajinFmt;
TrajectoryIO* tio = 0;
for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
ArgList args = argIn;
// Determine whether this file is multiple file or single file ensemble.
tio = TrajectoryFile::DetectFormat( *fn, trajinFmt );
if (tio == 0) {
mprinterr("Error: Could not determine trajectory %s format\n", fn->full());
err++;
continue;
}
EnsembleIn* ensemble = 0;
# ifdef ENABLE_SINGLE_ENSEMBLE
if (tio->CanProcessEnsemble())
ensemble = new EnsembleIn_Single();
else
# endif
ensemble = new EnsembleIn_Multi();
if (ensemble == 0) {
mprinterr("Error: Memory allocation for input ensemble failed.\n");
delete tio;
return 1;
}
ensemble->SetDebug( debug_ );
// CRDIDXARG: Append coordinate indices arg if there is one
args.AddArg( finalCrdIndicesArg_ );
if ( ensemble->SetupEnsembleRead(*fn, args, topIn) ) {
mprinterr("Error: Could not set up input ensemble '%s'.\n", fname.c_str());
delete ensemble;
delete tio;
err++;
continue;
}
// Currently all input ensembles must be same size.
if (ensembleSize_ == -1)
ensembleSize_ = ensemble->EnsembleCoordInfo().EnsembleSize();
else if (ensembleSize_ != ensemble->EnsembleCoordInfo().EnsembleSize()) {
mprinterr("Error: Ensemble size (%i) does not match first ensemble size (%i).\n",
ensemble->EnsembleCoordInfo().EnsembleSize(), ensembleSize_);
return 1;
}
// CRDIDXARG: If trajectory is REMD ensemble and sorting by CRDIDX, need to
// save final CRDIDX for next ensemble command.
// TODO: This is very clunky - remlog dataset should contain all exchanges
// so trajin doesnt have to worry about it.
# ifdef ENABLE_SINGLE_ENSEMBLE
if ( !tio->CanProcessEnsemble() ) {
# endif
EnsembleIn_Multi const& mTraj = static_cast<EnsembleIn_Multi const&>( *ensemble );
if ( mTraj.TargetMode() == ReplicaInfo::CRDIDX ) {
finalCrdIndicesArg_ = mTraj.FinalCrdIndices();
if (finalCrdIndicesArg_.empty()) {
mprinterr("Error: Could not obtain final remlog indices.\n");
delete ensemble;
delete tio;
err++;
continue;
}
//mprintf("DEBUG: Final crd indices arg: %s\n", finalCrdIndicesArg_.c_str());
}
# ifdef ENABLE_SINGLE_ENSEMBLE
} else
mprintf("Warning: Single ensemble cannot process crdidx.\n");
# endif
// Add to ensemble list and update # of frames.
ensemble_.push_back( ensemble );
UpdateMaxFrames( ensemble->Traj() );
delete tio;
}
if (err > 0) return 1;
// FIXME: For backwards compat. overwrite Topology box info with traj box info.
topIn->SetBoxFromTraj( ensemble_.back()->EnsembleCoordInfo().TrajBox() );
return 0;
}
/** Loop over all filenames in replica_filenames, set up TrajectoryIO. */
int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter,
CoordinateInfo& cInfo, Topology* trajParm)
{
// Sanity check
if (!IOarray_.empty()) {
mprinterr("Internal Error: SetupIOarray() has been called twice.\n");
return 1;
}
// Save arguments that have not been processed so they can be passed
// to each replica in turn. Only the lowest replica will use argIn.
ArgList argCopy( argIn );
bool lowestRep = true;
int rep0Frames = TrajectoryIO::TRAJIN_UNK; // Total frames in replica 0
int totalFrames = TrajectoryIO::TRAJIN_UNK; // Total # frames to be read from ensemble
TrajectoryFile::TrajFormatType lastRepFmt = TrajectoryFile::UNKNOWN_TRAJ;
// Right now enforce that all replicas have the same metadata as lowest
// replica, e.g. if replica 0 has temperature, replica 1 does too etc.
for (File::NameArray::const_iterator repfile = replica_filenames_.begin();
repfile != replica_filenames_.end(); ++repfile)
{
// Detect format
TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ;
TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( *repfile, repformat );
if ( replica0 == 0 ) {
mprinterr("Error: Could not set up replica file %s\n", repfile->full());
return 1;
}
if (repformat != lastRepFmt)
mprintf("\tReading '%s' as %s\n", repfile->full(), TrajectoryFile::FormatString(repformat));
lastRepFmt = repformat;
replica0->SetDebug( debug_ );
// Pushing replica0 here allows the destructor to handle it on errors
IOarray_.push_back( replica0 );
// Process format-specific read args. Do not exit on error in case
// replicas have different formats supporting different args.
if (lowestRep) {
replica0->processReadArgs( argIn );
} else {
ArgList argtmp( argCopy );
replica0->processReadArgs( argtmp );
}
// Set up replica for reading and get the number of frames.
int nframes = replica0->setupTrajin( *repfile, trajParm );
if (nframes == TrajectoryIO::TRAJIN_ERR) {
mprinterr("Error: Could not set up %s for reading.\n", repfile->full());
return 1;
}
// TODO: Do not allow unknown number of frames?
if (lowestRep) {
cInfo = replica0->CoordInfo();
rep0Frames = nframes;
totalFrames = nframes;
if (cInfo.ReplicaDimensions().Ndims() > 0) {
mprintf("\tReplica dimensions:\n");
for (int rd = 0; rd < cInfo.ReplicaDimensions().Ndims(); rd++)
mprintf("\t\t%i: %s\n", rd+1, cInfo.ReplicaDimensions().Description(rd));
}
} else {
// Check total frames in this replica against lowest rep.
if (nframes != rep0Frames)
mprintf("Warning: Replica %s frames (%i) does not match # frames in first replica (%i).\n",
repfile->base(), nframes, rep0Frames);
//if (repframes < 0) {
// mprinterr("Error: RemdTraj: Unknown # of frames in replica.\n");
// return 1;
//}
if (nframes < totalFrames) {
totalFrames = nframes;
mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n",
totalFrames);
}
// Check box info against lowest rep.
if ( replica0->CoordInfo().HasBox() != cInfo.HasBox() ) {
mprinterr("Error: Replica %s box info does not match first replica.\n",
repfile->full());
return 1;
}
// TODO: Check specific box type
// Check velocity info against lowest rep.
if ( replica0->CoordInfo().HasVel() != cInfo.HasVel() ) {
mprinterr("Error: Replica %s velocity info does not match first replica.\n",
repfile->full());
return 1;
}
// Check # dimensions and types against lowest rep
if ( replica0->CoordInfo().ReplicaDimensions() != cInfo.ReplicaDimensions() ) {
mprinterr("Error: Replica %s dimension info does not match first replica.\n",
repfile->full());
ReplicaDimArray const& thisRepDims = replica0->CoordInfo().ReplicaDimensions();
for (int rd = 0; rd < thisRepDims.Ndims(); rd++)
mprinterr("\t\t%i: %s\n", rd+1, thisRepDims.Description(rd));
return 1;
}
// If temperature/time info does not match set to false.
if (cInfo.HasTemp() != replica0->CoordInfo().HasTemp())
cInfo.SetTemperature( false );
if (cInfo.HasTime() != replica0->CoordInfo().HasTime())
cInfo.SetTime( false );
}
lowestRep = false;
}
// Check how many frames will actually be read
if (counter.CheckFrameArgs( totalFrames, argIn )) return 1;
// Check for errors.
if (IOarray_.empty()) {
mprinterr("Error: No replica trajectories set up.\n");
return 1;
}
if (IOarray_.size() != replica_filenames_.size()) { // SANITY CHECK
mprinterr("Error: Not all replica files were set up.\n");
return 1;
}
// Update ensemble size
cInfo.SetEnsembleSize( (int)IOarray_.size() );
if (debug_ > 0)
cInfo.PrintCoordInfo( replica_filenames_[0].full(), trajParm->c_str() );
return 0;
}
